A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
Report
generated on 2024-11-20, 12:09 PST
based on data in:
/gscratch/scrubbed/sr320/github/ceasmallr/output/04-bismark-align
General Statistics
| Sample Name | % Aligned | % Aligned |
|---|---|---|
| CF01-CM01-Zygote_R1_001 | 12.8% | |
| CF01-CM01-Zygote_stderr | 6.5% | |
| CF01-CM02-Larvae_R1_001 | 35.9% | |
| CF01-CM02-Larvae_stderr | 17.6% | |
| CF02-CM02-Zygote_R1_001 | 13.9% | |
| CF02-CM02-Zygote_stderr | 5.9% | |
| CF03-CM03-Zygote_R1_001 | 25.6% | |
| CF03-CM03-Zygote_stderr | 12.0% | |
| CF03-CM04-Larvae_PE_report | 46.1% | |
| CF03-CM04-Larvae_stderr | 22.0% | |
| CF03-CM05-Larvae_PE_report | 34.0% | |
| CF03-CM05-Larvae_stderr | 16.3% | |
| CF04-CM04-Zygote_PE_report | 25.1% | |
| CF04-CM04-Zygote_stderr | 11.2% | |
| CF05-CM02-Larvae_PE_report | 35.2% | |
| CF05-CM02-Larvae_stderr | 16.8% | |
| CF05-CM05-Zygote_PE_report | 25.3% | |
| CF05-CM05-Zygote_stderr | 13.1% | |
| CF06-CM01-Zygote_PE_report | 23.5% | |
| CF06-CM01-Zygote_stderr | 11.3% | |
| CF06-CM02-Larvae_PE_report | 22.7% | |
| CF06-CM02-Larvae_stderr | 11.0% | |
| CF07-CM02-Zygote_PE_report | 11.5% | |
| CF07-CM02-Zygote_stderr | 5.6% | |
| CF08-CM03-Zygote_PE_report | 18.9% | |
| CF08-CM03-Zygote_stderr | 7.9% | |
| CF08-CM04-Larvae_PE_report | 0.9% | |
| CF08-CM04-Larvae_stderr | 0.6% | |
| CF08-CM05-Larvae_PE_report | 2.1% | |
| CF08-CM05-Larvae_stderr | 1.1% | |
| EF01-EM01-Zygote_PE_report | 21.9% | |
| EF01-EM01-Zygote_stderr | 10.8% |
Bismark
0.24.2
Maps bisulfite converted sequence reads and determine cytosine methylation states.URL: http://www.bioinformatics.babraham.ac.uk/projects/bismarkDOI: 10.1093/bioinformatics/btr167
Alignment Rates
Strand Alignment
Bowtie 2 / HiSAT2
Results from both Bowtie 2 and HISAT2, tools for aligning reads against a reference genome.URL: http://bowtie-bio.sourceforge.net/bowtie2; https://ccb.jhu.edu/software/hisat2DOI: 10.1038/nmeth.1923; 10.1038/nmeth.3317; 10.1038/s41587-019-0201-4
Paired-end alignments
This plot shows the number of reads aligning to the reference in different ways.
There are 6 possible types of alignment:
- PE mapped uniquely: Pair has only one occurence in the reference genome.
- PE mapped discordantly uniquely: Pair has only one occurence but not in proper pair.
- PE one mate mapped uniquely: One read of a pair has one occurence.
- PE multimapped: Pair has multiple occurence.
- PE one mate multimapped: One read of a pair has multiple occurence.
- PE neither mate aligned: Pair has no occurence.
Software Versions
Software Versions lists versions of software tools extracted from file contents.
| Software | Version |
|---|---|
| Bismark | 0.24.2 |